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PMID: 29334380 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Light-activated chemical probing of nucleobase solvent accessibility inside cells.

Nature chemical biology ·Vol. 14 ·No. 3 ·2018-00-00 ·Pages 276-283

Feng C, Chan D, Joseph J, Muuronen M, Coldren WH, Dai N, Corrêa IR, Furche F, Hadad CM, Spitale RC

Abstract

The discovery of functional RNAs that are critical for normal and disease physiology continues to expand at a breakneck pace. Many RNA functions are controlled by the formation of specific structures, and an understanding of each structural component is necessary to elucidate its function. Measuring solvent accessibility intracellularly with experimental ease is an unmet need in the field. Here, we present a novel method for probing nucleobase solvent accessibility, Light Activated Structural Examination of RNA (LASER). LASER depends on light activation of a small molecule, nicotinoyl azide (NAz), to measure solvent accessibility of purine nucleobases. In vitro, this technique accurately monitors solvent accessibility and identifies rapid structural changes resulting from ligand binding in a metabolite-responsive RNA. LASER probing can further identify cellular RNA-protein interactions and unique intracellular RNA structures. Our photoactivation technique provides an adaptable framework to structurally characterize solvent accessibility of RNA in many environments.

MeSH Terms
Azides/chemistry Crystallography, X-Ray Guanosine/chemistry HeLa Cells Humans Hydrogen Bonding Ligands Light Molecular Biology Nucleic Acid Conformation Protein Binding Protein Folding Protein Interaction Mapping Purines/chemistry RNA/chemistry RNA, Ribosomal, 18S/chemistry Ribonucleoprotein, U1 Small Nuclear/chemistry Solvents/chemistry Thermoanaerobacter
Chemicals
Azides Ligands Purines RNA, Ribosomal, 18S Ribonucleoprotein, U1 Small Nuclear Solvents Guanosine RNA
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Feng Chao ORCID
Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA.
Chan Dalen
Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA.
Joseph Jojo
Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA.
Muuronen Mikko
Department of Chemistry, University of California, Irvine, Irvine, California, USA.
Coldren William H
Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA.
Dai Nan
New England BioLabs, Ipswich, Massachusetts, USA.
Corrêa Ivan R
New England BioLabs, Ipswich, Massachusetts, USA.
Furche Filipp
Department of Chemistry, University of California, Irvine, Irvine, California, USA.
Hadad Christopher M ORCID
Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA.
Spitale Robert C
Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA. | Department of Chemistry, University of California, Irvine, Irvine, California, USA.
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Article Info
Journal
Nature chemical biology
Abbr.
Nat Chem Biol
ISSN
1552-4469
DOI
10.1038/nchembio.2548
Published
2018-00-00
Epub
2018-00-15
Pages
276-283
Language
English
Region
United States
NLM ID
101231976
PMCID
PMC6203945
Subset
IM
Grants
NIGMS NIH HHS · DP2 GM119164 · United States
NIMH NIH HHS · R01 MH109588 · United States
Databases
PubChem-Substance
349974071, 349974074, 349974075, 349974076, 349974077, 349974078, 349974079, 349974080, 349974081, 349974072, 349974073
Corrections
ErratumIn
PMID: 29443971
CommentIn
PMID: 29443973
External Links
PubMed source DOI: 10.1038/nchembio.2548 PMC Full Text View journal details
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